SAXSdb — 7jmt

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1. Protein Identity and Related Structures Protein Identity & Related Structures

BCL-2 protein

Schistosoma japonicum

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 21–230	Not recorded	N3C 4-{4-[(4'-CHLOROBIPHENYL-2-YL)METHYL]PIPERAZIN-1-YL}-N-{[4-({(1R)-3-(DIMETHYLAMINO)-1-[(PHENYLTHIO)METHYL]PROPYL}AMINO)-3-NITROPHENYL]SULFONYL}BENZAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；sBCL-2:1, 1.6M dipotassium hydrogen phosphate, 0.4M sodium dihydrogen phosphate, 0.2M NaCl, 0.1M imidazole, pH8.0	Resolution 2.75 Å R-free 0.255
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 21–230	Not recorded	N3C 4-{4-[(4'-CHLOROBIPHENYL-2-YL)METHYL]PIPERAZIN-1-YL}-N-{[4-({(1R)-3-(DIMETHYLAMINO)-1-[(PHENYLTHIO)METHYL]PROPYL}AMINO)-3-NITROPHENYL]SULFONYL}BENZAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；sBCL-2:1, 1.6M dipotassium hydrogen phosphate, 0.4M sodium dihydrogen phosphate, 0.2M NaCl, 0.1M imidazole, pH8.0	Resolution 2.75 Å R-free 0.255
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 21–230	Not recorded	N3C 4-{4-[(4'-CHLOROBIPHENYL-2-YL)METHYL]PIPERAZIN-1-YL}-N-{[4-({(1R)-3-(DIMETHYLAMINO)-1-[(PHENYLTHIO)METHYL]PROPYL}AMINO)-3-NITROPHENYL]SULFONYL}BENZAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；sBCL-2:1, 1.6M dipotassium hydrogen phosphate, 0.4M sodium dihydrogen phosphate, 0.2M NaCl, 0.1M imidazole, pH8.0	Resolution 2.75 Å R-free 0.255
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 21–230	Not recorded	N3C 4-{4-[(4'-CHLOROBIPHENYL-2-YL)METHYL]PIPERAZIN-1-YL}-N-{[4-({(1R)-3-(DIMETHYLAMINO)-1-[(PHENYLTHIO)METHYL]PROPYL}AMINO)-3-NITROPHENYL]SULFONYL}BENZAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；sBCL-2:1, 1.6M dipotassium hydrogen phosphate, 0.4M sodium dihydrogen phosphate, 0.2M NaCl, 0.1M imidazole, pH8.0	Resolution 2.75 Å R-free 0.255
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 21–230	Not recorded	N3C 4-{4-[(4'-CHLOROBIPHENYL-2-YL)METHYL]PIPERAZIN-1-YL}-N-{[4-({(1R)-3-(DIMETHYLAMINO)-1-[(PHENYLTHIO)METHYL]PROPYL}AMINO)-3-NITROPHENYL]SULFONYL}BENZAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；sBCL-2:1, 1.6M dipotassium hydrogen phosphate, 0.4M sodium dihydrogen phosphate, 0.2M NaCl, 0.1M imidazole, pH8.0	Resolution 2.75 Å R-free 0.255
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 21–230	Not recorded	N3C 4-{4-[(4'-CHLOROBIPHENYL-2-YL)METHYL]PIPERAZIN-1-YL}-N-{[4-({(1R)-3-(DIMETHYLAMINO)-1-[(PHENYLTHIO)METHYL]PROPYL}AMINO)-3-NITROPHENYL]SULFONYL}BENZAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；sBCL-2:1, 1.6M dipotassium hydrogen phosphate, 0.4M sodium dihydrogen phosphate, 0.2M NaCl, 0.1M imidazole, pH8.0	Resolution 2.75 Å R-free 0.255

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 7JMT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3QBR BakBH3 in complex with sjA Deposited 2011-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 21–189（169 aa） Fragment：C-terminal truncation (RESIDUES 21-189)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；295 K；1M tri-sodium citrate, 0.1M CHES, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.60 Å R-free 0.234
3QBR BakBH3 in complex with sjA Deposited 2011-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 21–189（169 aa） Fragment：C-terminal truncation (RESIDUES 21-189)	Not recorded	NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；295 K；1M tri-sodium citrate, 0.1M CHES, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.60 Å R-free 0.234

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q5BWX6_SCHJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–210； UniProt 21–230 Author chain B； PDBConstruct 1–210； UniProt 21–230 Author chain C； PDBConstruct 1–210； UniProt 21–230 Author chain D； PDBConstruct 1–210； UniProt 21–230 Author chain E； PDBConstruct 1–210； UniProt 21–230 Author chain F； PDBConstruct 1–210； UniProt 21–230

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7jmt
Deposition date deposition_date	2020-08-02
Structure title title	Crystal structure of schistosome BCL-2 bound to ABT-737
Keywords keywords	APOPTOSIS; APOPTOSIS
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	38.17 Å
Radius of gyration Rg (electron density) rg_electron	37.13 Å
Forward intensity I(0) i0	176202000.00
Molecular weight molecular_weight	110320.0 kDa
Excluded volume excluded_volume	138970 Å³
Envelope volume envelope_volume	192970 Å³
Hydration-shell volume shell_volume	42268 Å³
Envelope diameter envelope_diameter	111.1 Å
Shell Rg shell_rg	45.10 Å
Envelope Rg envelope_rg	35.56 Å
Shape Rg shape_rg	37.11 Å
Total Rg total_rg	37.72 Å
Total atoms total_atoms	15158
Residues n_residues	955
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	111.8 Å
Rg (real space) rg_real	37.99 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	1.7620e+08
I(0) uncertainty (real space) i0_real_error	2.6110e+06
Rg (reciprocal space) rg_reciprocal	38.11 Å
I(0) (reciprocal space) i0_reciprocal	176200000.0000
Solution quality estimate total_estimate	0.8406
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	54.5 Å
Skewness Skewness skewness	0.005
Kurtosis Kurtosis kurtosis	-0.854
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	27280000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.976; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	BCL-2 protein
Molecular weight formula_weight	23416.7 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	15190

MSNTADFRLQTSTLCHSFLLASANKQDTDYLTDLLDNTNIDLTCVPNGQEIIHSLLQLVGDFNQRFSQTHEIEPVAQSLGIDSDKPVDKTALEIFYLEILNGLFEKLNWGRIVAMFAFLRILVLRLSKHGHSDAIQMLIKTTSQYSDEKLKNWINLHDGWSGLIEFSGRQFVNDGQELIWKTLRNVGGLATGAVGALGLAALVGYIANKI

来源 Source

来源生物 organism	Schistosoma japonicum
通用名 common_name	Blood fluke
NCBI Class编号 ncbi_taxonomy_id	6182
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	;4-{4-[(4'-CHLOROBIPHENYL-2-YL)METHYL]PIPERAZIN-1-YL}-N-{[4-({(1R)-3-(DIMETHYLAMINO)-1-[(PHENYLTHIO)METHYL]PROPYL}AMINO)-3-NITROPHENYL]SULFONYL}BENZAMIDE ;
Molecular weight formula_weight	813.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	32

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8. Citations (1)

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Unit-cell length a length_a	100.021 Å
Unit-cell length b length_b	67.789 Å
Unit-cell length c length_c	100.907 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	118.79 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	86.470 Å
R factor r_factor	0.2347
R_work r_work	0.2336
R_free r_free	0.2550

fit	/app/data/saxs_computation/jm/7jmt/7jmt.fit
pddf	/app/data/pr_computation/jm/7jmt/7jmt.pr.out
profile	/app/data/saxs_computation/jm/7jmt/7jmt.dat

Crystal structure of schistosome BCL-2 bound to ABT-737

1. Protein Identity and Related Structures Protein Identity & Related Structures

BCL-2 protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction